ChemoDOTS: a web server to design chemistry-driven focused libraries.

In drug discovery, the successful optimization of an initial hit compound into a lead molecule requires multiple cycles of chemical modification. Consequently, there is a need to efficiently generate synthesizable chemical libraries to navigate the chemical space surrounding the primary hit. To address this need, we introduce ChemoDOTS, an easy-to-use web server for hit-to-lead chemical optimization freely available at https://chemodots.marseille.inserm.fr/. With this tool, users enter an activated form of the initial hit molecule then choose from automatically detected reactive functions. The server proposes compatible chemical transformations via an ensemble of encoded chemical reactions widely used in the pharmaceutical industry during hit-to-lead optimization. After selection of the desired reactions, all compatible chemical building blocks are automatically coupled to the initial hit to generate a raw chemical library. Post-processing filters can be applied to extract a subset of compounds with specific physicochemical properties. Finally, explicit stereoisomers and tautomers are computed, and a 3D conformer is generated for each molecule. The resulting virtual library is compatible with most docking software for virtual screening campaigns. ChemoDOTS rapidly generates synthetically feasible, hit-focused, large, diverse chemical libraries with finely-tuned physicochemical properties via a user-friendly interface providing a powerful resource for researchers engaged in hit-to-lead optimization.

Mechanism of head-to-head MCM double-hexamer formation revealed by cryo-EM.

In preparation for bidirectional DNA replication, the origin recognition complex (ORC) loads two hexameric MCM helicases to form a head-to-head double hexamer around DNA1,2. The mechanism of MCM double-hexamer formation is debated. Single-molecule experiments have suggested a sequential mechanism, in which the ORC-dependent loading of the first hexamer drives the recruitment of the second hexamer3. By contrast, biochemical data have shown that two rings are loaded independently via the same ORC-mediated mechanism, at two inverted DNA sites4,5. Here we visualize MCM loading using time-resolved electron microscopy, and identify intermediates in the formation of the double hexamer. We confirm that both hexamers are recruited via the same interaction that occurs between ORC and the C-terminal domains of the MCM helicases. Moreover, we identify the mechanism of coupled MCM loading. The loading of the first MCM hexamer around DNA creates a distinct interaction site, which promotes the engagement of ORC at the N-terminal homodimerization interface of MCM. In this configuration, ORC is poised to direct the recruitment of the second hexamer in an inverted orientation, which is suitable for the formation of the double hexamer. Our results therefore reconcile the two apparently contrasting models derived from single-molecule experiments and biochemical data.

Production of phosphorene nanoribbons.

Phosphorene is a mono-elemental, two-dimensional (2D) substance with outstanding, highly directional properties and a bandgap that depends on the number of layers of the material1-8. Nanoribbons, meanwhile, combine the flexibility and unidirectional properties of one-dimensional nanomaterials, the high surface area of 2D nanomaterials and the electron-confinement and edge effects of both. The structures of nanoribbons can thus lead to exceptional control over electronic band structure, the emergence of novel phenomena and unique architectures for applications5,6,9-24. Phosphorene's intrinsically anisotropic structure has motivated numerous theoretical calculations of phosphorene nanoribbons (PNRs), predicting extraordinary properties5,6,12-24. So far, however, discrete PNRs have not been produced. Here we present a method for creating quantities of high-quality, individual PNRs by ionic scissoring of macroscopic black phosphorus crystals. This top-down process results in stable liquid dispersions of PNRs with typical widths of 4-50 nm, predominantly single-layer thickness, measured lengths of up to 75 µm and aspect ratios of up to 1,000. The nanoribbons are atomically flat single crystals, aligned exclusively in the zigzag crystallographic orientation. The ribbons have remarkably uniform widths along their entire lengths, and are extremely flexible. These properties-together with the ease of downstream manipulation via liquid-phase methods-should enable the search for predicted exotic states6,12-14,17-19,21, and an array of applications in which PNRs have been predicted to offer transformative advantages. These applications range from thermoelectric devices to high-capacity fast-charging batteries and integrated high-speed electronic circuits6,14-16,20,23,24.

Informing geometric deep learning with electronic interactions to accelerate quantum chemistry.

Predicting electronic energies, densities, and related chemical properties can facilitate the discovery of novel catalysts, medicines, and battery materials. However, existing machine learning techniques are challenged by the scarcity of training data when exploring unknown chemical spaces. We overcome this barrier by systematically incorporating knowledge of molecular electronic structure into deep learning. By developing a physics-inspired equivariant neural network, we introduce a method to learn molecular representations based on the electronic interactions among atomic orbitals. Our method, OrbNet-Equi, leverages efficient tight-binding simulations and learned mappings to recover high-fidelity physical quantities. OrbNet-Equi accurately models a wide spectrum of target properties while being several orders of magnitude faster than density functional theory. Despite only using training samples collected from readily available small-molecule libraries, OrbNet-Equi outperforms traditional semiempirical and machine learning-based methods on comprehensive downstream benchmarks that encompass diverse main-group chemical processes. Our method also describes interactions in challenging charge-transfer complexes and open-shell systems. We anticipate that the strategy presented here will help to expand opportunities for studies in chemistry and materials science, where the acquisition of experimental or reference training data is costly.

Preclinical translational platform of neuroinflammatory disease biology relevant to neurodegenerative disease.

Neuroinflammation is a key driver of neurodegenerative disease, however the tools available to model this disease biology at the systems level are lacking. We describe a translational drug discovery platform based on organotypic culture of murine cortical brain slices that recapitulate disease-relevant neuroinflammatory biology. After an acute injury response, the brain slices assume a chronic neuroinflammatory state marked by transcriptomic profiles indicative of activation of microglia and astrocytes and loss of neuronal function. Microglia are necessary for manifestation of this neuroinflammation, as depletion of microglia prior to isolation of the brain slices prevents both activation of astrocytes and robust loss of synaptic function genes. The transcriptomic pattern of neuroinflammation in the mouse platform is present in published datasets derived from patients with amyotrophic lateral sclerosis, Huntington's disease, and frontotemporal dementia. Pharmacological utility of the platform was validated by demonstrating reversal of microglial activation and the overall transcriptomic signature with transforming growth factor-ß. Additional anti-inflammatory targets were screened and inhibitors of glucocorticoid receptors, COX-2, dihydrofolate reductase, and NLRP3 inflammasome all failed to reverse the neuroinflammatory signature. Bioinformatics analysis of the neuroinflammatory signature identified protein tyrosine phosphatase non-receptor type 11 (PTPN11/SHP2) as a potential target. Three structurally distinct inhibitors of PTPN11 (RMC-4550, TN0155, IACS-13909) reversed the neuroinflammatory disease signature. Collectively, these results highlight the utility of this novel neuroinflammatory platform for facilitating identification and validation of targets for neuroinflammatory neurodegenerative disease drug discovery.

Closing the Chasm: Understanding and Addressing the Anesthesia Workforce Supply and Demand Imbalance.

The imbalance in anesthesia workforce supply and demand has been exacerbated post-COVID due to a surge in demand for anesthesia care, especially in non-operating room anesthetizing sites, at a faster rate than the increase in anesthesia clinicians. The consequences of this imbalance or labor shortage compromise healthcare facilities, adversely affect the cost of care, worsen anesthesia workforce burnout, disrupt procedural and surgical schedules, and threaten academic missions and the ability to educate future anesthesiologists. In developing possible solutions, one must examine emerging trends that are affecting the anesthesia workforce, new technologies that will transform anesthesia care and the workforce, and financial considerations, including governmental payment policies. Possible practice solutions to this imbalance will require both short- and long-term multifactorial approaches that include increasing training positions and retention policies, improving capacity through innovations, leveraging technology, and addressing financial constraints.

Reversal of Propofol-induced Depression of the Hypoxic Ventilatory Response by BK-channel Blocker ENA-001: A Randomized Controlled Trial.

BACKGROUND: The use of anesthetics may result in depression of the hypoxic ventilatory response. Since there are no receptor-specific antagonists for most anesthetics, there is the need for agnostic respiratory stimulants that increase respiratory drive irrespective of its cause. The authors tested whether ENA-001, an agnostic respiratory stimulant that blocks carotid body BK-channels, could restore the hypoxic ventilatory response during propofol infusion. They hypothesize that ENA-001 is able to fully restore the hypoxic ventilatory response. METHODS: In this randomized, double-blind crossover trial, 14 male and female healthy volunteers were randomized to receive placebo and low- and high-dose ENA-001 on three separate occasions. On each occasion, isohypercapnic hypoxic ventilatory responses were measured during a fixed sequence of placebo, followed by low- and high-dose propofol infusion. The authors conducted a population pharmacokinetic/pharmacodynamic analysis that included oxygen and carbon dioxide kinetics. RESULTS: Twelve subjects completed the three sessions; no serious adverse events occurred. The propofol concentrations were 0.6 and 2.0 µg/ml at low and high dose, respectively. The ENA-001 concentrations were 0.6 and 1.0 µg/ml at low and high dose, respectively. The propofol concentration that reduced the hypoxic ventilatory response by 50% was 1.47 ± 0.20 µg/ml. The steady state ENA-001 concentration to increase the depressed ventilatory response by 50% was 0.51 ± 0.04 µg/ml. A concentration of 1 µg/ml ENA-001 was required for full reversal of the propofol effect at the propofol concentration that reduced the hypoxic ventilatory response by 50%. CONCLUSIONS: In this pilot study, the authors demonstrated that ENA-001 restored the hypoxic ventilatory response impaired by propofol. This finding is not only of clinical importance but also provides mechanistic insights into the peripheral stimulation of breathing with ENA-001 overcoming central depression by propofol.

The associative ionization of N(2P) + O(3P).

The rate constant of the associative ionization reaction N(2P) + O(3P) → NO+ + e- was measured using a flow tube apparatus. A flowing afterglow source was used to produce an ion/electron plasma containing a mixture of ions, including N2+, N3+, and N4+. Dissociative recombination of these species produced a population of nitrogen atoms, including N(2P). Charged species were rejected from the flow tube using an electrostatic grid, subsequent to which oxygen atoms were introduced, produced either using a discharge of helium and oxygen or via the titration of nitrogen atoms with NO. Only the title reaction can produce the NO+ observed after the introduction of O atoms. The resulting rate constant (8 ± 5 ×10-11 cm3 s-1) is larger than previously reported N(2P) + O disappearance rate constants (∼2 × 10-11 cm3 s-1). The possible errors in this or previous experiments are discussed. It is concluded that the N(2P) + O(3P) reaction proceeds almost entirely by associative ionization, with quenching to the 2D or 4S states as only minor processes.

Development of the data registry for the Cardiac Neurodevelopmental Outcome Collaborative.

Children with congenital heart disease (CHD) can face neurodevelopmental, psychological, and behavioural difficulties beginning in infancy and continuing through adulthood. Despite overall improvements in medical care and a growing focus on neurodevelopmental screening and evaluation in recent years, neurodevelopmental disabilities, delays, and deficits remain a concern. The Cardiac Neurodevelopmental Outcome Collaborative was founded in 2016 with the goal of improving neurodevelopmental outcomes for individuals with CHD and pediatric heart disease. This paper describes the establishment of a centralised clinical data registry to standardize data collection across member institutions of the Cardiac Neurodevelopmental Outcome Collaborative. The goal of this registry is to foster collaboration for large, multi-centre research and quality improvement initiatives that will benefit individuals and families with CHD and improve their quality of life. We describe the components of the registry, initial research projects proposed using data from the registry, and lessons learned in the development of the registry.

Nanoscale Ultrafine Zinc Metal Anodes for High Stability Aqueous Zinc Ion Batteries.

Aqueous Zn batteries (AZBs) are a promising energy storage technology, due to their high theoretical capacity, low redox potential, and safety. However, dendrite growth and parasitic reactions occurring at the surface of metallic Zn result in severe instability. Here we report a new method to achieve ultrafine Zn nanograin anodes by using ethylene glycol monomethyl ether (EGME) molecules to manipulate zinc nucleation and growth processes. It is demonstrated that EGME complexes with Zn2+ to moderately increase the driving force for nucleation, as well as adsorbs on the Zn surface to prevent H-corrosion and dendritic protuberances by refining the grains. As a result, the nanoscale anode delivers high Coulombic efficiency (ca. 99.5%), long-term cycle life (over 366 days and 8800 cycles), and outstanding compatibility with state-of-the-art cathodes (ZnVO and AC) in full cells. This work offers a new route for interfacial engineering in aqueous metal-ion batteries, with significant implications for the commercial future of AZBs.

Antiretroviral Therapy Intensification for Neurocognitive Impairment in Human Immunodeficiency Virus.

BACKGROUND: Neurocognitive impairment (NCI) in people with HIV (PWH) on antiretroviral therapy (ART) is common and may result from persistent HIV replication in the central nervous system. METHODS: A5324 was a randomized, double-blind, placebo-controlled, 96-week trial of ART intensification with dolutegravir (DTG) + MVC, DTG + Placebo, or Dual - Placebo in PWH with plasma HIV RNA <50 copies/mL on ART and NCI. The primary outcome was the change on the normalized total z score (ie, the mean of individual NC test z scores) at week 48. RESULTS: Of 357 screened, 191 enrolled: 71% male, 51% Black race, 22% Hispanic ethnicity; mean age 52 years; mean CD4+ T-cells 681 cells/µL. Most (65%) had symptomatic HIV-associated NC disorder. Study drug was discontinued due to an adverse event in 15 (8%) and did not differ between arms (P = .17). Total z score, depressive symptoms, and daily functioning improved over time in all arms with no significant differences between them at week 48 or later. Adjusting for age, sex, race, study site, efavirenz use, or baseline z score did not alter the results. Body mass index modestly increased over 96 weeks (mean increase 0.32 kg/m2, P = .006) and did not differ between arms (P > .10). CONCLUSIONS: This is the largest, randomized, placebo-controlled trial of ART intensification for NCI in PWH. The findings do not support empiric ART intensification as a treatment for NCI in PWH on suppressive ART. They also do not support that DTG adversely affects cognition, mood, or weight.

Surgery versus Conservative Care for Persistent Sciatica Lasting 4 to 12 Months.

BACKGROUND: The treatment of chronic sciatica caused by herniation of a lumbar disk has not been well studied in comparison with acute disk herniation. Data are needed on whether diskectomy or a conservative approach is better for sciatica that has persisted for several months. METHODS: In a single-center trial, we randomly assigned patients with sciatica that had lasted for 4 to 12 months and lumbar disk herniation at the L4-L5 or L5-S1 level in a 1:1 ratio to undergo microdiskectomy or to receive 6 months of standardized nonoperative care followed by surgery if needed. Surgery was performed by spine surgeons who used conventional microdiskectomy techniques. The primary outcome was the intensity of leg pain on a visual analogue scale (ranging from 0 to 10, with higher scores indicating more severe pain) at 6 months after enrollment. Secondary outcomes were the score on the Oswestry Disability Index, back and leg pain, and quality-of-life scores at 6 weeks, 3 months, 6 months, and 1 year. RESULTS: From 2010 through 2016, a total of 790 patients were screened; of those patients, 128 were enrolled, with 64 in each group. Among the patients assigned to undergo surgery, the median time from randomization to surgery was 3.1 weeks; of the 64 patients in the nonsurgical group, 22 (34%) crossed over to undergo surgery at a median of 11 months after enrollment. At baseline, the mean score for leg-pain intensity was 7.7 in the surgical group and 8.0 in the nonsurgical group. The primary outcome of the leg-pain intensity score at 6 months was 2.8 in the surgical group and 5.2 in the nonsurgical group (adjusted mean difference, 2.4; 95% confidence interval, 1.4 to 3.4; P<0.001). Secondary outcomes including the score on the Owestry Disability Index and pain at 12 months were in the same direction as the primary outcome. Nine patients had adverse events associated with surgery, and one patient underwent repeat surgery for recurrent disk herniation. CONCLUSIONS: In this single-center trial involving patients with sciatica lasting more than 4 months and caused by lumbar disk herniation, microdiskectomy was superior to nonsurgical care with respect to pain intensity at 6 months of follow-up. (Funded by Physicians' Services Incorporated Foundation; ClinicalTrials.gov number, NCT01335646.).

Disentangling water, ion and polymer dynamics in an anion exchange membrane.

Semipermeable polymeric anion exchange membranes are essential for separation, filtration and energy conversion technologies including reverse electrodialysis systems that produce energy from salinity gradients, fuel cells to generate electrical power from the electrochemical reaction between hydrogen and oxygen, and water electrolyser systems that provide H2 fuel. Anion exchange membrane fuel cells and anion exchange membrane water electrolysers rely on the membrane to transport OH- ions between the cathode and anode in a process that involves cooperative interactions with H2O molecules and polymer dynamics. Understanding and controlling the interactions between the relaxation and diffusional processes pose a main scientific and critical membrane design challenge. Here quasi-elastic neutron scattering is applied over a wide range of timescales (100-103 ps) to disentangle the water, polymer relaxation and OH- diffusional dynamics in commercially available anion exchange membranes (Fumatech FAD-55) designed for selective anion transport across different technology platforms, using the concept of serial decoupling of relaxation and diffusional processes to analyse the data. Preliminary data are also reported for a laboratory-prepared anion exchange membrane especially designed for fuel cell applications.

The local ordering of polar solvents around crystalline carbon nitride nanosheets in solution.

The crystalline graphitic carbon nitride, poly-triazine imide (PTI) is highly unusual among layered materials since it is spontaneously soluble in aprotic, polar solvents including dimethylformamide (DMF). The PTI material consists of layers of carbon nitride intercalated with LiBr. When dissolved, the resulting solutions consist of dissolved, luminescent single to multilayer nanosheets of around 60-125 nm in diameter and Li+ and Br- ions originating from the intercalating salt. To understand this unique solubility, the structure of these solutions has been investigated by high-energy X-ray and neutron diffraction. Although the diffraction patterns are dominated by inter-solvent correlations there are clear differences between the X-ray diffraction data of the PTI solution and the solvent in the 4-6 Å-1 range, with real space differences persisting to at least 10 Å. Structural modelling using both neutron and X-ray datasets as a constraint reveal the formation of distinct, dense solvation shells surrounding the nanoparticles with a layer of Br-close to the PTI-solvent interface. This solvent ordering provides a configuration that is energetically favourable underpinning thermodynamically driven PTI dissolution. This article is part of the theme issue 'Exploring the length scales, timescales and chemistry of challenging materials (Part 2)'.

Amphoteric dissolution of two-dimensional polytriazine imide carbon nitrides in water.

Crystalline two-dimensional carbon nitrides with polytriazine imide (PTI) structure are shown to act amphoterically, buffering both HCl and NaOH aqueous solutions, resulting in charged PTI layers that dissolve spontaneously in their aqueous media, particularly for the alkaline solutions. This provides a low energy, green route to their scalable solution processing. Protonation in acid is shown to occur at pyridinic nitrogens, stabilized by adjacent triazines, whereas deprotonation in base occurs primarily at basal plane NH bridges, although NH2 edge deprotonation is competitive. We conclude that mildly acidic or basic pHs are necessary to provide sufficient net charge on the nanosheets to promote dissolution, while avoiding high ion concentrations which screen the repulsion of like-charged PTI sheets in solution. This article is part of the theme issue 'Exploring the length scales, timescales and chemistry of challenging materials (Part 2)'.

Kinetics of associative detachment of O- + N2 and dissociative attachment of e- + N2O up to 1300 K: chemistry relevant to modeling of transient luminous events.

The rate constants of O- + N2 → N2O + e- from 800 K to 1200 K and the reverse process e- + N2O → O- + N2 from 700 K to 1300 K are measured using a flowing afterglow - Langmuir probe apparatus. The rate constants for O- + N2 are well described by 3 × 10-12 e-0.28 eV kT-1 cm3 s-1. The rate constants for e- + N2O are somewhat larger than previously reported and are well described by 7 × 10-7 e-0.48 eV kT-1 cm3 s-1. The resulting equilibrium constants differ from those calculated using the fundamental thermodynamics by factors of 2-3, likely due to significantly non-thermal product distributions in one or both reactions. The potential surfaces of N2O and N2O- are calculated at the CCSD(T) level. The minimum energy crossing point is identified 0.53 eV above the N2O minimum, similar to the activation energy for the electron attachment to N2O. A barrier between N2O- and O- + N2 is also identified with a transition state at a similar energy of 0.52 eV. The activation energy of O- + N2 is similar to one vibrational quantum of N2. The calculated potential surface supports the notion that vibrational excitation will enhance reaction above the same energy in translation, and vibrational-state specific rate constants are derived from the data. The O- + N2 rate constants are much smaller than literature values measured in a drift tube apparatus, supporting the contention that those values were overestimated due to the presence of vibrationally excited N2. The result impacts the modeling of transient luminous events in the mesosphere.

Spasticity Management Teams, Evaluations, and Tools: A Canadian Cross-Sectional Survey.

OBJECTIVE: The objective of this study is to determine the physical evaluations and assessment tools used by a group of Canadian healthcare professionals treating adults with spasticity. METHODS: A cross-sectional web-based 19-question survey was developed to determine the types of physical evaluations, tone-related impairment measurements, and assessment tools used in the management of adults with spasticity. The survey was distributed to healthcare professionals from the Canadian Advances in Neuro-Orthopedics for Spasticity Congress database. RESULTS: Eighty study participants (61 physiatrists and 19 other healthcare professionals) completed the survey and were included. Nearly half (46.3%, 37/80) of the participants reported having an inter- or trans-disciplinary team managing individuals with spasticity. Visual observation of movement, available range of motion determination, tone during velocity-dependent passive range of motion looking for a spastic catch, spasticity, and clonus, and evaluation of gait were the most frequently used physical evaluations. The most frequently used spasticity tools were the Modified Ashworth Scale, goniometer, and Goal Attainment Scale. Results were similar in brain- and spinal cord-predominant etiologies. To evaluate goals, qualitative description was used most (37.5%). CONCLUSION: Our findings provide a better understanding of the spasticity management landscape in Canada with respect to staffing, physical evaluations, and outcome measurements used in clinical practice. For all etiologies of spasticity, visual observation of patient movement, Modified Ashworth Scale, and qualitative goal outcomes descriptions were most commonly used to guide treatment and optimize outcomes. Understanding the current practice of spasticity assessment will help provide guidance for clinical evaluation and management of spasticity.

Electron and Ar+ interaction with Mo(CO)6 at thermal energies; energetic limit on removal of 5 ligands from Mo(CO)6.

The rate constant for electron attachment to Mo(CO)6 was determined to be ka = 2.4 ± 0.6 × 10-7 cm3 s-1 at 297 K in a flowing-afterglow Langmuir-probe experiment. The sole anion product is Mo(CO)5-. A small decline in ka was observed up to 450 K, and decomposition was apparent at higher temperatures. The charge transfer reaction of Ar+ with Mo(CO)6 is exothermic by 7.59 ± 0.03 eV, which appears to be sufficient to remove the first 5 ligands from Mo(CO)6+.

Clinical presentation of exercise-associated hyponatremia in male and female IRONMAN® triathletes over three decades.

PURPOSE: Exercise-associated hyponatremia (EAH) is common in ultra-endurance events and severe cases are more common in females. The purpose of this paper is to compare the clinical presentation of EAH between male and female triathletes in ultra-endurance competitions. METHODS: Medical records with sodium concentrations (n = 3138) from the IRONMAN® World Championships over the timeframe of 1989-2019 were reviewed for both male (n = 2253) and female (n = 885) competitors. Logistic regression was used to explore the relationships between sex, sodium concentration, and various clinical presentations. RESULTS: When comparing male and female triathletes, clinical variables found to have a different relationship with sodium concentration include altered mental status (inversely related in males and not related in females), abdominal pain, muscle cramps, hypotension, and tachycardia (directly related in males and not related in females), and vomiting and hypokalemia (not related in males and inversely related in females). Overall, males lost significantly more weight than females, and notably, approximately half of all athletes were dehydrated and lost weight. CONCLUSIONS: Altered mental status, vomiting, abdominal pain, muscle cramps, hypotension, tachycardia, and hyperkalemia appear to present differently between sexes when comparing hyponatremic to eunatremic athletes. Although overhydration is the most common etiology of hypervolemic hyponatremia, hypovolemic hyponatremia comprises a significant amount of hyponatremic triathletes. Further understanding of how EAH presents helps athletes and medical professionals identify it early and prevent life-threatening complications.

Coordination of -1 programmed ribosomal frameshifting by transcript and nascent chain features revealed by deep mutational scanning.

Programmed ribosomal frameshifting (PRF) is a translational recoding mechanism that enables the synthesis of multiple polypeptides from a single transcript. During translation of the alphavirus structural polyprotein, the efficiency of -1PRF is coordinated by a 'slippery' sequence in the transcript, an adjacent RNA stem-loop, and a conformational transition in the nascent polypeptide chain. To characterize each of these effectors, we measured the effects of 4530 mutations on -1PRF by deep mutational scanning. While most mutations within the slip-site and stem-loop reduce the efficiency of -1PRF, the effects of mutations upstream of the slip-site are far more variable. We identify several regions where modifications of the amino acid sequence of the nascent polypeptide impact the efficiency of -1PRF. Molecular dynamics simulations of polyprotein biogenesis suggest the effects of these mutations primarily arise from their impacts on the mechanical forces that are generated by the translocon-mediated cotranslational folding of the nascent polypeptide chain. Finally, we provide evidence suggesting that the coupling between cotranslational folding and -1PRF depends on the translation kinetics upstream of the slip-site. These findings demonstrate how -1PRF is coordinated by features within both the transcript and nascent chain.